The invention relates generally to analyzing autoradiograms for relatedness of materials distributed in rows on the autoradiograms and, more specifically, to a computer-assisted apparatus for automatically analyzing autoradiograms and generating similarity coefficients between rows which are presented as a matrix, as a histogram, as a dendrogram, or as any combination thereof.
Gel electrophoresis is useful for sorting molecules by size. Mixtures containing proteins of different sizes, RNA's of different sizes, or DNA fragments of different sizes are loaded on gels and separated electrophoretically. In the case of DNA fragments, the major application of this invention, DNA fragments are separated primarily according to size with smaller fragments closer to the anode. The fragments are hybridized with a radiolabeled tag, usually a moderately repetitive sequence. By placing a sheet of X-ray film adjacent to the gel, or a blot of the gel, bands are resolved which correspond to fragments hybridized with the radiolabeled probe. This provides a pattern of bands, differing in size and intensity, which can be analyzed and compared visually by a researcher or optically by a scanner.
Although analysis of DNA fragments by gel electrophoresis is used for many purposes, analysis of banding patterns is most commonly used to "fingerprint" organisms such as viruses, bacteria, fungi, plants and, more recently, animals, including humans. DNA fingerprinting is useful for testing whether particular genetic sequences are present or are polymorphic, and so may be used as an epidemiological tool for following the etiological vector of a particular infection, identifying the source of infection, identifying a genetically based disease, or measuring the genetic similarity of two individuals, or strains, in a common species.
The characterization of strains of microorganisms is most widely accomplished by collecting and comparing phenotypic traits such as serotypes, resistance to chemicals, assimilation patterns, and colony or streak morphology. Phenotypic-based characterization systems, however, run the risk of grouping strains of microorganisms that are phenotypically similar but genetically unrelated. The converse, separating genetically related strains that are phenotypically dissimilar, can also result. DNA fingerprinting provides a far more meaningful route for typing strains since it compares genetic rather than phenotypic information. Unfortunately, the analysis of autoradiograms requires a great deal of time and effort. Moreover, autoradiograms often produce rows, or lanes of bands, which curve or are distorted, including lanes of differing length, lanes in which corresponding bands of the same fragments are resolved at shifted locations, variations in band intensity between runs, and so on. Considerable experience and skill is often required of the researcher, accordingly, to ensure that a valid analysis is being performed. Further, the human visual analysis process is inherently subjective such that differences in analysis may occur between researchers, and very limited when the number of strains being compared increases dramatically.
The specification of this invention includes a microfiche appendix under 37 C.F.R. .sctn.1.96 of 3 microfiche comprising a total of 281 frames. The appendix is a print-out in object code of the computer software program which is a part of this invention.